<tool id="rpscore" name="Score Pathway" version="5.9.2">
    <description>Computes a global score for a heterologous pathway.</description>
	<requirements>
        <requirement type="package" version="5.9.2">rptools</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
	    python -m rptools.rpscore '$pathway' '$scored_pathway'
        --no_of_rxns_thres '$adv.no_of_rxns_thres'
        --log '$adv.log_level'
    ]]></command>
    <inputs>
		<param name="pathway" type="data" format="xml" label="Pathway (rpSBML)" />
		<section name="adv" title="Advanced Options" expanded="false">
            <param name="no_of_rxns_thres" type="integer" value="10" label="number of reactions above which a pathway is not scored" />
			<param name="log_level"      type="select"  label="Log level">
                <option value="debug"                    >debug</option>
                <option value="info"                     >info</option>
			    <option value="warning"                  >warning</option>
			    <option value="error"     selected="true">error</option>
			    <option value="critical"                 >critical</option>
            </param>
		</section>
    </inputs>
    <outputs>
        <data name="scored_pathway" format="xml" label="${tool.name} - ${pathway.name}" />
    </outputs>
    <tests>
        <test>
        <!-- test 1: check if identical outputs are produced with default parameters  -->
            <param name="pathway" value="pathway.xml" />
            <output name="scored_pathway" file="scored_pathway.xml" ftype="xml" compare="diff" sort="true"/>
        </test>
    </tests>
    <help><![CDATA[
rpscore
=========


Computes a global score for a heterologous pathway. The score is calculated from a learning process based on reaction rules score, flux balance analysis and thermodynamics metrics, and the number of reactions in the pathway.


Input
-----

Required:

* **infile**\ : (string) Pathway file (rpSBML) with scores (rules, FBA, Thermo...)
* **outfile**\ : (string) Path to write pathway file (rpSBML) with global score

Advanced options:

* **--no_of_rxns_thres**\ :(integer, default: 10) Number of reactions above which pathway are not scored (too long)
* **--log**: (string, default=error) Set the log level, choices are 'debug', 'info', 'warning', 'error', 'critical'

Version
----------

5.9.2

Authors
-------

* **Jean-Loup Faulon**
* **Joan Hérisson**

Acknowledgments
---------------

* Thomas Duigou
    ]]></help>
</tool>